The uniqueness of Elliðaár rivers, situated in Reykjavík is reflected by their origin from the lake Elliðavatn to their estuary, both being within the city limit. Few studies have been carried out on the rivers and lake microbial diversity. The objective of this study was to screen the microbial diversity and presence of faecal indicators in the rivers and lake. Samples were taken from three sampling sites in the lake and six sampling sites in the rivers four times over a nine-month period. Total viable count was estimated using flow cytometry and traditional culturing methods following incubation at 4°C and 30°C. The indicator species Escherichia coli, Enterococcus spp. and norovirus were used to estimate faecal pollution. Diversity of uncultured bacteria was analysed using the 16S rRNA gene sequencing method. The lake and rivers were categorised according to provisions in regulation no. 796/1999 on water pollution. The results indicate that the nearby urban area considerably influences the water quality of the lake and rivers. High faecal pollution caused by E. coli was measured in the lake and some parts of the rivers, and noroviruses were detected on three other sites, indicating faecal pollution. The lake was categorised as type D, “very polluted”, and the rivers type B, “little pollution”, on average. The microbial diversity depicted using the 16S rRNA gene sequencing method was quite diverse and differed between sampling sites. The method identified bacteria that are prevailing in natural freshwater and two genera were detected in all samples; Flavobacterium spp. and Limnohabitans spp.